Understanding 3D genome organization by multidisciplinary methods
I Jerkovic, G Cavalli - Nature Reviews Molecular Cell Biology, 2021 - nature.com
Understanding how chromatin is folded in the nucleus is fundamental to understanding its
function. Although 3D genome organization has been historically difficult to study owing to a …
function. Although 3D genome organization has been historically difficult to study owing to a …
Hi-C analysis: from data generation to integration
In the epigenetics field, large-scale functional genomics datasets of ever-increasing size and
complexity have been produced using experimental techniques based on high-throughput …
complexity have been produced using experimental techniques based on high-throughput …
Comparison of computational methods for the identification of topologically associating domains
M Zufferey, D Tavernari, E Oricchio, G Ciriello - Genome biology, 2018 - Springer
Background Chromatin folding gives rise to structural elements among which are clusters of
densely interacting DNA regions termed topologically associating domains (TADs). TADs …
densely interacting DNA regions termed topologically associating domains (TADs). TADs …
Stratification of TAD boundaries reveals preferential insulation of super-enhancers by strong boundaries
The metazoan genome is compartmentalized in areas of highly interacting chromatin known
as topologically associating domains (TADs). TADs are demarcated by boundaries mostly …
as topologically associating domains (TADs). TADs are demarcated by boundaries mostly …
Interphase human chromosome exhibits out of equilibrium glassy dynamics
Fingerprints of the three-dimensional organization of genomes have emerged using
advances in Hi-C and imaging techniques. However, genome dynamics is poorly …
advances in Hi-C and imaging techniques. However, genome dynamics is poorly …
Decoding topologically associating domains with ultra-low resolution Hi-C data by graph structural entropy
A Li, X Yin, B Xu, D Wang, J Han, Y Wei, Y Deng… - Nature …, 2018 - nature.com
Submegabase-size topologically associating domains (TAD) have been observed in high-
throughput chromatin interaction data (Hi-C). However, accurate detection of TADs depends …
throughput chromatin interaction data (Hi-C). However, accurate detection of TADs depends …
Reference panel guided topological structure annotation of Hi-C data
Y Zhang, M Blanchette - Nature Communications, 2022 - nature.com
Accurately annotating topological structures (eg, loops and topologically associating
domains) from Hi-C data is critical for understanding the role of 3D genome organization in …
domains) from Hi-C data is critical for understanding the role of 3D genome organization in …
Applicability and interpretability of Ward's hierarchical agglomerative clustering with or without contiguity constraints
N Randriamihamison, N Vialaneix, P Neuvial - Journal of Classification, 2021 - Springer
Hierarchical agglomerative clustering (HAC) with Ward's linkage has been widely used
since its introduction by Ward (Journal of the American Statistical Association, 58 (301), 236 …
since its introduction by Ward (Journal of the American Statistical Association, 58 (301), 236 …
OnTAD: hierarchical domain structure reveals the divergence of activity among TADs and boundaries
The spatial organization of chromatin in the nucleus has been implicated in regulating gene
expression. Maps of high-frequency interactions between different segments of chromatin …
expression. Maps of high-frequency interactions between different segments of chromatin …
How epigenome drives chromatin folding and dynamics, insights from efficient coarse-grained models of chromosomes
The 3D organization of chromosomes is crucial for regulating gene expression and cell
function. Many experimental and polymer modeling efforts are dedicated to deciphering the …
function. Many experimental and polymer modeling efforts are dedicated to deciphering the …